| Variant ID: vg0811599488 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 11599488 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
CCGGCGGACGAGTCCAGTGCGCCCTGCGGCTCGGCGATGGTGTGTTCGGCGGCTGCGAGGCGGGCGGCTAGGTCGCCCTGGCCCGCGGCCGCCCCGCCGC[T/C]
GTGCGCTCTCGCGTCCAGCTCCTTCGCCCGCGCCTCGAGCTCAGCGGCCCGCTGATCCAGTGCGGCCCTCTCGGCGCGGACGCCTTCCAGATTGCGGCGC
GCGCCGCAATCTGGAAGGCGTCCGCGCCGAGAGGGCCGCACTGGATCAGCGGGCCGCTGAGCTCGAGGCGCGGGCGAAGGAGCTGGACGCGAGAGCGCAC[A/G]
GCGGCGGGGCGGCCGCGGGCCAGGGCGACCTAGCCGCCCGCCTCGCAGCCGCCGAACACACCATCGCCGAGCCGCAGGGCGCACTGGACTCGTCCGCCGG
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 0.50% | 0.10% | 2.94% | 96.42% | NA |
| All Indica | 2759 | 0.80% | 0.00% | 2.07% | 97.06% | NA |
| All Japonica | 1512 | 0.00% | 0.10% | 4.89% | 94.97% | NA |
| Aus | 269 | 0.00% | 0.70% | 1.86% | 97.40% | NA |
| Indica I | 595 | 0.20% | 0.00% | 0.34% | 99.50% | NA |
| Indica II | 465 | 0.00% | 0.00% | 0.22% | 99.78% | NA |
| Indica III | 913 | 1.80% | 0.10% | 5.26% | 92.88% | NA |
| Indica Intermediate | 786 | 0.80% | 0.00% | 0.76% | 98.47% | NA |
| Temperate Japonica | 767 | 0.00% | 0.10% | 6.26% | 93.61% | NA |
| Tropical Japonica | 504 | 0.00% | 0.20% | 3.77% | 96.03% | NA |
| Japonica Intermediate | 241 | 0.00% | 0.00% | 2.90% | 97.10% | NA |
| VI/Aromatic | 96 | 0.00% | 1.00% | 1.04% | 97.92% | NA |
| Intermediate | 90 | 1.10% | 0.00% | 2.22% | 96.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0811599488 | T -> C | LOC_Os08g19400.1 | missense_variant ; p.Ser139Gly; MODERATE | nonsynonymous_codon ; S139G | Average:19.773; most accessible tissue: Zhenshan97 root, score: 32.766 | unknown | unknown | DELETERIOUS | 0.03 |
| vg0811599488 | T -> DEL | LOC_Os08g19400.1 | N | frameshift_variant | Average:19.773; most accessible tissue: Zhenshan97 root, score: 32.766 | N | N | N | N |